The Trindade and Martin Vaz island group (TMVIG) is located at about 1,120 km off the Brazilian coast. Despite its importance, highlighted by the presence of several endemic fish species, the TMVIG lacks detailed information on the structure of fish and benthic assemblages. Presented here is the first quantitative assessment of reef fish and benthic assemblages of the TMVIG in a depth gradient ranging from 5 to 45 m. Additional qualitative information on reef assemblages between 45 and 100 m was obtained using advanced gas diving techniques (TRIMIX) and a remotely operated vehicle (ROV). Similarly to other Brazilian oceanic islands, the TMVIG possesses depauperated fish and benthic assemblages, possibly due to its isolation and small size in comparison to the mainland. Depth was the most important factor affecting the structure of fish assemblages, with the density of most fish species declining with depth. Deep reefs (> 45 m) were characterized by the presence of extensive rhodolith beds and rocky reefs sparsely covered with crustose coralline algae, black coral (Cirripathes sp.) and a few massive or plate-like reef corals. Part-time or obligatory planktivorous fishes (e.g. Cephalopholis furcifer and Clepticus brasiliensis) also dominated deep reefs. Similar characteristics were recorded in mesophotic reef ecosystems across the Western Atlantic. Evidence of overfishing (obtained here and in other recent studies), the presence of four endemic and restricted range fish species, as well as the increase in number of new (and still undescribed) endemic taxa, indicates that the adoption of precautionary conservation measures are urgently needed in order to maintain the fragile and unique ecosystems of the TMVIG.